3ZE9

3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms

PDB DOI: https://doi.org/10.2210/pdb3ZE9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Mutation(s): Yes

Deposited: 2012-12-03 Released: 2013-06-12
Deposition Author(s): Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.148
R-Value Work: 0.131
R-Value Observed: 0.132

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough

Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.

(2013) Int J Hydrogen Energy 38: 8664

DOI: https://doi.org/10.1016/J.IJHYDENE.2013.04.132

Macromolecule Content

Total Structure Weight: 85.08 kDa
Atom Count: 6,802
Modelled Residue Count: 761
Deposited Residue Count: 768
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT	A	283	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 EC: 1.12.7.2
UniProt
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS4 Go to UniProtKB: Q72AS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72AS4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING	B	484	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 1 EC: 1.12.7.2
UniProt
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS3 Go to UniProtKB: Q72AS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72AS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSX Query on FSX Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) Fe₄ O₃ S₃ BIOGFUMNBIDAOG-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
FCO Query on FCO Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS
OCS Query on OCS	B	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS
PSW Query on PSW	B	L-PEPTIDE LINKING	C₃ H₇ N O₂ S Se		SEC

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.148
R-Value Work: 0.131
R-Value Observed: 0.132
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.694	α = 90
b = 63.348	β = 105.42
c = 109.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2014-02-19
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description
Version 1.2: 2014-05-14
Changes: Atomic model
Version 1.3: 2014-11-05
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
Version 1.4: 2018-06-27
Changes: Advisory, Data collection, Derived calculations
Version 2.0: 2019-04-24
Changes: Atomic model, Data collection, Experimental preparation, Polymer sequence
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description